The first level follows the sequence of events of the Star Trek: Voyager episode Endgame. Voyager, having entered the Borg transwarp network, is in a route to Earth at unimaginable speeds, but has been caught by a Borg sphere and trapped inside. It is up to the Hazard Team, led by Lt. Munro, with Chell, Chang, and Telsia to beam into the sphere and utilize every bit of knowledge about the Borg to free the vessel before it is assimilated. When the team first beams on the sphere, they are separated, leaving Munro only with Chang. After quickly finding Chell behind a forcefield, the team of three engage in a small battle with several Borg drones. Chang is captured, preparing to be assimilated. Additionally, the I-MOD, the only weapon the Borg cannot adapt to, is taken offline by a dampener. Fortunately, Munro finds Chang and orders him beamed back to Voyager. After continuing through the sphere with Chell, Telsia is found, and they all proceed to restore their I-MODs and get Voyager out of the dampener field. When they succeed, Munro orders all three of them to beam out. However, Munro is sent back to the Borg Central Plexus. After defeating a newer, larger, and technologically improved Borg drone, Munro is sent back to Voyager. Voyager is then seen escaping back to the Alpha Quadrant.

Having returned to the Alpha Quadrant, Munro is assigned by Starfleet to teach at the Academy. Skipping ahead two years to 2380, we see Munro teaching his Klingon student Korban in a holodeck program about defending and escaping a Klingon outpost from Romulans. At the end of the program, they leave the holodeck to see their session had been observed by CaptainJean-Luc Picard. He is interested in the idea of a Hazard Team for the USS Enterprise, and organizes Munro's transfer.

Before Munro can settle in on the Enterprise, they receive a distress call from the USS Dallas, an Excelsior class starship in orbit of an Attrexian station. The Attrexians are a race of beings seeking Federation membership. Boarding the vessel in environmental suits, Munro, Chell, Jurot, and a new addition, Franklin, must get the vessel back online and find out what happened to it, as well as being reunited with an old friend - Telsia Murphy, one of Munro's former partners on the Voyager Hazard Team. In this mission, Franklin is killed when being pulled out of a ceiling by an unknown creature.

Realizing the Dallas was attacked by a creature who can chew through a tritanium hull while responding to a distress call from the Attrexians, Munro and his team are shuttled down to the station to protect the Attrexians and to try and find out more about the creatures. Munro meets a soon-to-be member of the Hazard Team, Jorge Gonzales.

Following the ion trail from the creature's impulse drive after being forced out of the station, they find an Idryll planet, a primitive slave race of the Attrexians who believe they existed before the Attrexians. Meeting some Idryll scientists, the Hazard Team find out the creatures, known as Exomorphs, are manufactured from the raw materials in the planet's core as slaves, but have malfunctioned to become 'evil'.

Responding to another distress call from another Attrexian colony, the Enterprise warps in to see an Idryll ship waiting for them. The Hazard Team prepare to beam down, but the Idryll ship opens fire on the Enterprise when the shields were lowered. Picard discovers the Idryll are under Krindo's command - one of the scientists from the Idryll planet (the last level) who is furious that his colleague Kleeya chose to stay on the Enterprise to help stop the Exomorphs and to stay with Lt. Munro. Intruders beam in, and the Hazard Team deploy to fight off Krindo's forces.

Finally able to shuttle down to the Attrexian planet, the Hazard team render whatever aid they can. Munro does find a Idyll shuttle, containing Krindo's father, who was said to have saved many Attrexians.

Tracking Krindo to a nearby planet, and with the Enterprise under repair, the Hazard Team shuttle to the Idryll planet after him. Krindo only stops the attacks when he realizes his father is helping the Attrexians on the planet under attack.

Krindo confesses he made money to fund his expedition by selling priceless artifacts and secrets of the expedition to a Ferengi. Krindo surmises that the Ferengi decoded the location of the Master Control Facility, which can override all other Exomorph controls. After arranging to meet this Ferengi on an old Starbase, he is captured by the Hazard Team.

The Ferengi eventually divulges he sold the location of the Master Control Facility to a group of Romulans calling themselves the Empty Crown. Munro infiltrates the base of the Empty Crown, and discovers the location of the Master Control Facility, at the cost of Gonzales's life.

Although no stardate is given for the events of the game, the first level takes place when Voyager returned to the Alpha Quadrant in 2377 or 2378. By skipping ahead two years, that would place most of the events in this game in the year 2379 or 2380, which is after or concurrent to the events of Star Trek: Nemesis.

One of the complaints that received much vocalization[citation needed](who?) after the release of this game was the lack of Next Generation cast members present, compared to the previous game, which had all the members of Voyager's principal cast involved. Because this game could take place after Nemesis, the lack of TNG cast members should be explained as follows:

This is the first appearance of a Denobulan in a Star Trek video game.

Actor Derek McGrath, who played Chell in the episodes of Star Trek: Voyager and the first Elite Force, is replaced by Andy Milder, who previously played a Bolian engineer in Star Trek: Bridge Commander. Most of the other characters are voiced by the same actors as the first game.

The game has a Star Wars reference at the old Klingon starbase where a male Andorian and female Klingon are negotiating with a Human smuggler. The Andorian is asking for a large starship to carry two crew members, ten canisters and no questions asked with half latinum paid then and another half later which is paraphrased from the Cantina scene of Star Wars IV: A New Hope when Obi-Wan Kenobi is negotiating with Han Solo for transport.

There is a reference TNGepisode: "Chain of Command", in a scene where two Romulans discuss how long their Starfleet prisoner will last before cracking. One of the Romulans commenting that a Starfleet prisoner was capable of breaking even a Cardassian interrogator.